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Ancient DNA: today’s lecture

  • Molecular phylogenetics
  • Ancient DNA
  • Sabretooth cats
  • Sequencing the North Sea Homotherium

Molecular phylogenetics

Molecular phylogenetics

  • This is called a phylogeny
  • It represents the evolutionary process
  • The phylogeny is like an evolutionary tree
  • The tips are species
  • Nodes are their common ancestors
  • Molecular phylogenies are based on DNA data

Mutation and inheritance creates the tree

  • Human mutation rate ~1.1×10−8 per site per generation
  • Human: ~40 mutations in your 3.6 Gb genome

  • DNA divergence and time are (approximately) linearly related
  • Branch lengths show the genetic divergence

DNA sequence alignment

Mitochondrial DNA is great for phylogenetics!


  • Small genome (~16,000 base pair)
  • High mutation rate
  • Many copies per cell
  • Maternally inherited
  • No recombination

Ancient DNA

“Ancient DNA” is just old DNA

Some samples don’t fit in the lab!

Allows study of extinct species!

*Glyptodont, WolfmanSF, CC BY_SA 3.0*

Glyptodont, WolfmanSF, CC BY_SA 3.0

After thousands of years, most DNA is lost

*Zátonyi Sándor, CC BY-SA 3.0*

Zátonyi Sándor, CC BY-SA 3.0

This makes the work contamination sensitive

*Copyright Karla Fritze, Potsdam University*

Copyright Karla Fritze, Potsdam University

But the samples are already contaminated

*Data from Noonan et al. 2005. Science*

Data from Noonan et al. 2005. Science

Sabretooth cats

There were multiple genera of sabretooth cats

  • A genus is a group of closely related species. It’s the first part of the scientific name
  • e.g. Homo sapiens

Smilodon

  • The most commonly known group
  • Massive canines
  • Up to 400 kg and 120 cm shoulder height
  • N and S America
  • 3 species, S. gracilis, S. populator, S. fatalis
  • Extinction 10 Ka (“Kilo annum”)


*Sergiodlarosa, CC BY-SA 3.0*

Sergiodlarosa, CC BY-SA 3.0

Homotherium

  • Less known group
  • Also known as scimitar-toothed cats
  • Flat, serrated canines
  • ~ 200 kg and 110 cm shoulder height
  • Europe, Africa, N and S America
  • Pleistocene Europe: H. latidens, extinction 300 Ka
  • Pleistocene N. America: H. serum, extinction 12 Ka


*Sergiodlarosa, CC BY-SA 3.0*

Sergiodlarosa, CC BY-SA 3.0

Pleistocene sabretooth cats

Fishing for fossils

  • Britain connected to mainland Europe by an area called Doggerland
  • Rising sea levels 6-7 ka flooded the area, making Britain an island

16th March 2000, something turned up…

→ This didn’t look like a 300 Ka fossil!

Dating of the Dutch North Sea Homotherium

  • The bone was radiocarbon dated at 31,300 ± 400!
  • This was extraordinary, so the dating was repeated
  • New dates:
    • 31,300 ± 400
    • 26,900 ± 400
    • 26,700 ± 240
    • 28,100 ± 220
    • 27,650 ± 280
  • The first Late Pleistocene European Homotherium

Didn’t fit in the picture!

DNA analysis of North Sea Homotherium

Sequencing of ancient DNA

Sequencing experiment 1

  • Total sequences = 2,628,309
  • Homotherium sequences grand total =
  • 1     😂

DNA hybridisation capture

  • DNA has 2 strands, arrange in a double helix
  • It can be heat denatured
  • When cooled, the single strands will stick (hybridise) to strands with a similar sequence
  • We can “fish” target sequences from a pool of contaminants


DNA hybridisation capture*

→ *Of course this only works if you know the sequence in advance!

Mistaken identity

Meanwhile a Danish group were sequencing North American cave lion DNA

  • Sequence analysis showed it was actually a Homotherium!
  • This provided the sequence for the hybridisation cature baits


Sequencing experiment 2
(hybridisation capture)

  • Total sequences = 72,759,982
  • Homotherium sequences grand total =
  • 12,050,089     🎉
  • 3 Homotherium and 1 Smilodon mitochondrial genomes

Phylogenetic analysis of sabretooth cats

Mutation and inheritance creates the tree

  • Human mutation rate ~1.1×10−8 per site per generation
  • Human: ~40 mutations in your 3.6 Gb genome

  • DNA divergence and time are (approximately) linearly related
  • Branch lengths show the genetic divergence

Molecular dating of sabretooth cats

Molecular dating of sabretooth cats

Molecular dating of sabretooth cats

  • Sabretooths divergence from living cats 20 Ma
  • Homotherium and Smilodon were more diverged from one another than any living cats
  • A huge diversity was lost with the extinction of the sabretooths
  • North American and European Homotherium were genetically similar
  • We recommended they be treated as a single species, H. latidens

Paijmans et al. 2017

Thank you for listening!